From The Beginning
by BlackLouie
Summary: Ho-oh was the first Johto legendary to be discovered along with Lugia. When humans and pokemon's bonds start to shatter there is only one thing that Ho-oh can do... He creates three legendary beasts giving them their pokemon names and giving them a quest. Now with the beasts running around, the world of pokemon might have a chance to be saved...
1. Ho-oh's Creations

**Hello this is another Pokemon story but I wanted to make this one cannon. This story takes place far into the past before Ash was even thought about, along with Misty and Brock. So bare with me! I'm not too good with writing, there are things I could improve on so if you find anything wrong, nicely tell me on how I can improve on it or have me change a few things here and there. Thanks! Enjoy!**

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 _Legends say that there is a world where humans and pokemon live together, in peace, harmony and through hard times. In this world, there are many pokemon that have loving bonds with their respective trainers and they each hold that bond until the end of time..._

 _Pokemon and humans go through many challenges, many good times and bad times, but no matter what... Peace is still out there for everyone, even if they are alone..._

Somewhere in Johto...

Lightning crashes through the sky while rain pours down in the town of Johto, people driving in cars are stuck in traffic after long hours of work. Some cars trapped in floods as a female officer is helping them all out of the cars as the townsfolk run home in the rain or seek shelter at the Pokemon Center with their pokemon.

The officer wiped her forehead after getting a young boy and his mother out of the stuck car. She saw a explosion from a distance, she looked at the blast with a surprised look on her face and she gasped.

"Who? Or what?" She was going to question it, but the rain was still pouring, she figured that she would be all wet before it was all over. She didn't want to get sick, so she hurried home herself and stayed out of the flooded areas.

From the flooded waters, a small baby pokemon rose from it's currents, it's purple mane blowing in the harsh wind of the storm as it cried out. It tried to crawl up to the sidewalk of the wet town, it turned it's head to it's right and saw a box. It crawled over to it, wet and a little cold from the pouring rain. The baby pokemon watched the rain drops fall to the ground on the sidewalk, it wasn't surprised by this since it just rose up from the water.

It decided to rest in the box for shelter, the poor little pokemon needed it. It would also need food to survive, seeing how dangerous the weather was, it was going to run off the next day...

* * *

In the forest of Johto...

Fire was growing from the lightning that struck the breach of the forest. Forest pokemon were running for shelter, scared of the flames. Stantler were running in heards as the Pidgeys were flying in the air to get away from the fire. A young Cyndaquil was scared of the flames, thought it was a fire type, the huge flames were making strange shapes that it didn't understand too well. The rain wasn't enough to keep it down as a small brown furred pokemon rose from it. It tried to mewel but it couldn't, it crawled from the fire and made it's way to a cave for shelter. Once it was there, it rested and fell asleep.

From afar, lightning struck the dirt, coming from the lightning was another baby pokemon, its yellow and black fur twitching as it rose from the lightning and crawled away to a nearby cave for shelter, but a Flaffy bumped into the baby pokemon, knocking it off balance, the Flaffy was scared, a person was going after it in the rain. It didn't make sense, but the young pokemon had to find shelter so that it didn't get sick from being out in the cold rain.

* * *

The next morning...

In a tall building in the town of Johto...

A researcher set out to find a new batch of legendary pokemon along with a few rare ones. He's kept his book for 45 years and it was going to be 46 years. He wanted to please his boss on finding new pokemon. The researcher's name was Professer Rein, he was going to become an expert soon as he wanted to draw and write about the pokemon and their special abilities.

His boss was down on the first floor, waiting for him. Professer Rein packed up his note book and his things for his research and headed down the stairs of the building and met his boss at the bottom.

"Hey Ray! I'm going out now!" Rein called to his boss.

"Wait! Before you go, let me update your dex, you will need room to type in the information of the pokemon as you keep special notes and drawings in your book. This will help us create the images of the pokemon for the dex itself." Ray explained while updating Rein's dex.

He handed the dex back to him.

"Now, you be careful out there. It can be dangerous. Also, try not to trip in mud, and watch out for high puddles." Ray chuckled.

"Don't worry, Ray. I'll be fine!" Rein rushed out of the door and hurried off into the forest to find new Pokemon. He heard many people talking about the strom from last night, he didn't even want to know about it since he's been through the storms.

He made his way through the park and down the path towards the forest. He stopped and took out his note book, in case he saw a pokemon that he needed to draw.

"Alright... I must be care now... Many pokemon might look nice, but they can be fierce at times." Rein was thinking about how he was chased by a Rhydon while making the discovery of Zapdos, Moltress and Articuno. This was going to be no different in his mind.

He kept on going, slowly and carefully this time...

* * *

In the meadows of Johto...

Three baby pokemon were squealing away, it was the same ones that rose from the lightning, fire and water. They opened their eyes and yawned, they were sleeping in the middle of the meadow. The young ones looked at each other for a long time before finally saying something.

 _"Who are you?"_ The blue pokemon asked, it's mane and two tails from it's behind were moving a bit in the wind.

 _"I don't know who I am..."_ The brown furred pokemon replied, he was so young, it was like he was born yesterday.

 _"I'm just born?"_ The yellow pokemon shook a bit and ran around, the brown furred one finally giggled and played with the yellow pokemon. The blue only sat down and felt the wind blow up against him.

Suddenly, something big was flying in the sky, it was circling them, trying to find a good place to land as a rainbow wing fell from it's feathers and landed on the young pokemon's nose. He sneezed as the feather lightly floated to the ground as it layed on the soft grass. The blue pokemon sniffed it carefully.

Finally the huge pokemon landed in front of his face, looking at him. Eyes were locked. The other two stopped playing to see the huge bird pokemon as it looked down on them. It's wings spread out as it spoke.

" _Hello... I am Ho-oh."_ The bird spoke up, the young ones were confused and tilted their heads.

 _"H-Ho-oh? What is a Ho-oh?"_ The yellow pokemon asked, he was confused.

 _"I'm Ho-Oh. I have created you three... You see there is a tower that keeps me coming when I hear the four silver crystal bells ring. You three have a huge mission and I will need your help, things seem like they're fine, but they are not..."_ Ho-oh squawked.

" _Mission? Like a fun thing?"_ The brown furred pokemon squealed with excited before the blue one interrupted him.

 _"No... It's like a serious thing?"_ The blue could tell from Ho-oh's tone that their mission was urgent.

 _"Yes, this is serious... You three must help me watch over the humans and the other pokemon, stop pokemon and humans from fighting each other, learn your abilities and learn where you shall one day live..."_ Ho-oh answered him.

They all didn't understand, but it was going to be a tough journey for the three of them.

 _"Do not be afraid... You all are still young, you were born yesterday and I shall give you all your pokemon names... Yellow one, you will be known as Raikou. Brown one, you will be known as Entei and you, my blue friend will be known as Suicune... Your abilities are unknown, you must find your powers on your own, I cannot supply you with them. This is farewell, we will meet again some day..."_ Ho-oh explained the final detail of his information and flew away, back to his home.

Raikou, Entei and Suicune watched him until he was seen no more. They all were confused on where they should go, they looked to the north and saw a huge tower like building. It interested them in someway. Entei finally spoke up.

" _Can we head over there?_ " Entei wondered.

" _Maybe... It does look like a cool place to explore._ " Raikou tensed up and walked ahead, leaving Suicune speechless. He followed the two and listened to them talk the whole way. From behind Rein was coming, he looked around and saw three small pokemon walking to the north of the medows. He took out his pencil and wrote down what the pokemon looked like, he lost sight of them as he followed them.

"I have to find out what pokemon they are! I bet my boss would be happy to see these guys! It will also be my first discovery since the legendary Ho-oh came into my sight!" Rein was excited. He looked over the hill and saw nothing. He was confused.

"I could have sworn I saw three pokemon." He scratched his head and looked left and right, he looked in the bushes and behind trees. From the distance, Suicune was seeing the human.

" _You guys need to keep back, well, we need to keep back."_ Suicune calmy stated.

" _Why? What's wrong with a human?"_ Entei was looking at Rein.

" _How do you know we won't get hurt?"_ Suicune looked at Entei sternly for a moment before sighing.

Raikou listened to them argue over the matter, he finally got up and peeked from the bushes, he didn't see Rein anymore.

" _He's gone, I think we can keep going._ " Raikou hissed, he carefully moved in case the researcher was hiding behind something. Then he fully came out of the bushes, he beckoned both his partners to come out. Suicune and Entei did so, but carefully.

" _The faster we reach that tower, the better._ " Entei smiled. Raikou and Suicune nodded in agreement.

The legendary beasts were born! And the first ones to be in the world! Ho-oh's first creations were going to watch over all humans and pokemon once they find their abilities and their own purposes...

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 **To be continued...**

 **Please don't forget to review this. This story is cannon to the anime I suppose... But I wanted to add a twist to it. I would always picture Ho-oh creating the beasts so that he had watchers besides himself. So I hope you guys tag along for this long ride, I don't know how many chapters this will have but I will try my best to come up with ideas for this one. ^w^**


	2. Worse Outcomes

**Well I'm working on this a bunch with ideas, so if things look rushed, please let me know. I will be able to add things to the chapter much later when I get better ideas! And thanks to the two users that let me know about the people on here that are very crazy about how things should be written! I'm not new to the community because I've written about 5 or 6 stories on pokemon, I deleted some of the stories because they made no sense, but I have kept some of the ones I liked because they were written very well! I'm still working on "The Hunter VS The Beast" with a female Raikou, it's got 3 chapters already, I'm working on the 4th chapter, I just need more ideas...**

 **Anyway, Enjoy the chapter!**

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The three young legendary beasts headed north, but they kept a low profile. Suicune jumped when a Caterpie was moving towards him, he looked at it before catching up with Entei and Raikou. Raikou looked back and noticed that a shiny rainbow thing was in the mane of Suicune, he stopped. Entei turned and saw that Raikou stopped in front of Suicune.

" _What is that thing in your mane? Do you mind explaining?_ " Raikou was looking at him suspiciously. Suicune closed his eyes, trying to remain calm as he answered his question.

" _It's a rainbow feather, it dropped from Ho-oh when he landed._ " Suicune shook the feather out of his mane, it slowly floated to the ground. Entei studied it and sniffed the feather, it had a nice sweet scent to it.

" _So is this ours to keep?_ "Entei wondered, Suicune shrugged, he didn't know if they were supposed to have it with them, but he had Raikou place it back in his mane.

" _I think it is safe with you._ "Raikou nodded while grabbing the feather in his teeth and placing it back in Suicune's purple mane, Suicune smiled when Raikou gave him back the Rainbow Wing.

" _If we keep the rainbow feather, we should be able to learn our abilities I bet."_ Entei explained.

" _I thought it was a way to remember Ho-oh by..."_ Raikou was now confused, he looked back at Suicune, who could only shrug once again.

" _It could be a gift, a small gift and I want to keep it."_ Suicune replied to the situation. They finally kept moving, they heard the cries of other pokemon and the sound of human voices, the peeked from each bush and turned every corner of the forest. Entei was leading the way, he saw a couple of Metepods spitting out webs at a Tyranitar that was attacking them.

" _God, why are they fighting? That's all I'm hearing."_ Entei growled, he wanted to leap in and stop the fight, but he knew it was too small to jump in, he would have to wait until the time was right.

" _It's best if we don't get in their way..."_ Raikou suggested, Entei nodded but Suicune disagreed with it all. He wanted to do something about the fight.

" _I'm going to stop them, I don't want them to fight like that._ " Suicune stepped past Raikou and Entei, he leaped from the other end of the bushes, Raikou and Entei watched quietly, they saw Suicune mewel at them.

" _Oh! Who is this?"_ One of the Metepods asked. The other ones started to calm down, for some reason, seeing Suicune stopped them from fighting, it's like they knew they were wrong for shooting webs at the Tyranitar.

" _Oh my god, thank you..._ " Tyranitar sighed with relief, Suicune released an glow of power as the webs disappeared from the body of the big dragon like pokemon.

" _What did I just do? Did I release this pokemon with my powers?_ " Suicune was confused, the Tyranitar walked away, not even turning back to look at Suicune again as he grunted, he was angry with the bug pokemon for messing with him for no reason.

Entei and Raikou walked up to the confused Suicune. The water type beast turned his head and saw them coming.

" _That power that you used was awesome!_ " Entei cheerfully added.

" _Where did you learn that?_ " Raikou asked.

" _I... I don't know... I just did it..._ " Suicune shyly stated.

Could it have been the Rainbow Wing? Did Ho-oh lend them their powers with it, or was it luck? Suicune couldn't stop thinking about the power that he released. Finally, Entei beckoned them to follow him on their long journey.

Raikou leaped up on some rocks, a cliff was blocking their way and they had to climb up carefully, one slip could be fatal for them all. Suicune was behind him and Entei was last, he wanted to make sure that the other two were okay since he was the leader. Once Suicune and Raikou made it above the cliff, Entei had help from them, his weight being too heavy.

Once Entei was with them again, they continued through a cave, it was dark, but it was the only way they could get to the tower. Suicune turned around and saw that the light was getting dimmer the further they walked into the cave. Raikou couldn't see ahead at all as something came out of his eyes, it was light.

" _Whoa! I can see, can you guys see?_ " Raikou exclaimed, Suicune and Entei nodded.

" _We can see, how are you doing that?_ " Suicune asked him, Raikou didn't know as Entei only smiled at this.

" _We seem to be learning fast._ " Entei commented, Raikou kept on going, the move Flash was keeping things in order as they were able to see things in the cave. Suicune was also hearing the sound of human trainers yelling, they sounded like they were in trouble.

" _Do you all hear that?_ " Raikou asked while looking ahead. Suicune and Entei nodded.

" _It sounds like humans and a few pokemon._ " Suicune growled, he didn't want to break up another fight, he didn't want to hurt anyone.

" _I think I will handle them this time._ " Entei turned to Suicune. This made the water type beast feel better. He didn't want to use some other power that could cause danger to the humans and the pokemon.

* * *

In the middle of the cave...

Two pokemon trainers were trying to keep the Shroomish away, they were using stunspore on their pokemon. The Pikachu and the Eevee were in danger of the evil Shroomish, they chirped and tried to attack the trainers. Entei saw this and let out a blast of fire from his mouth in anger. Raikou and Suicune gasped, the flames barely missed the trainers and the Shroomish, Pikachu and Eevee were safe as they hid behind their trainers after being stunned for a while. The Shroomish got scared and looked at Entei, they finally calmed down and left the trainers and their pokemon alone. Both of the trainers turned and looked at the small Entei.

"Hey... Did you do that?" One of the trainer who was a female asked, she was about 14 years old. The small Entei nodded at her, she bent down to pet him when a shock of lightning struck her hand, she quickly pulled it back. Raikou also found his new power.

"Hey, what gives!?" The male trainer asked as he gasped, seeing that there was two more beasts. He back away from them a few inches, he was afraid of them even though they were baby pokemon.

"Ouch... My hand..." The female trainer rubbed her hand. She looked up and saw what shocked her, it was the baby Raikou. The little Suicune was by his side.

"Is your hand okay?" The male trainer asked his friend, she turned and nodded at him, finally Suicune came up to her and licked her hand, then he gave a stern look at Raikou. Raikou only shrugged.

" _What? She was touching Entei!_ " Raikou growled.

" _I'm okay with that, Raikou._ " Entei replied to his mean comment. Raikou only grumbled and allowed the trainers to pet him, he purred when the male trainer finally came over and scratched his chin.

"These little ones are cute." The male trainer smiled, he was 15 years old.

"They are, I wonder what they are doing here all alone. Do you think we should take them with us? I mean we can get them to safety." The female trainer picked up Suicune, this made the beast feel shy. He blushed and looked down at Entei and Raikou for help.

" _She is holding me? What should I do?_ " Suicune was asking them, Entei wanted to tell him to wait while Raikou was unsure of what to do. He only watched. Finally the male trainer picked up both Entei and Raikou, they both blushed as well.

"I think we should take them home with us and have them stay for a while until we can release them. Right now. there are too many angry pokemon running around. It's like peace has been broken." The male trainer replied to his friend's question.

"Alright, let's go home!" The female trainer grinned, she hugged Suicune tight, the beast wanted to be put down but he didn't want to harm the trainers. They were humans, and his mind was telling him that. Entei and Raikou calmly went along with what Suicune was doing, they wanted to know where they were going.

The Pikachu and the Eevee followed their trainers on foot, they didn't mind walking as they knew their trainers would not be able to hold more than two pokemon at a time.

"Pika!" The Pikachu cheerfully squealed.

"Eevee!" Eevee smiled at the Pikachu, they were having their own conversation as usual when they were together.

"Oh? I guess you will be keeping the Suicune with you, right?" The male trainer asked her.

"Yes, I will keep him with me, but when the time comes, we will meet each other back at the cave entrance, Jerry." The female trainer replied.

"Alright, I don't know anything about these pokemon, but in case they get big, we should let them go when the time is right." Jerry sighed.

Once they made it back to their side of town, they went their separate ways. Pikachu, Entei, Raikou and Jerry were going to the left while Eevee, Suicune and Maria walked to the right, since she lived a few blocks down. Suicune was not comfortable without Entei or Raikou around him. Was this part of Ho-oh's plan? To keep them with trainers, to help them get humans and pokemon back together? He was worried about his friends. He would miss them for a little while.

Raikou was more worried about Suicune, he looked at Entei, the fire type beast didn't know what to do. He was calm about it and the look he gave Raikou was a look of keeping a low profile since they were going home with an unknown being.

Once they got to the house, Raikou rolled his eyes and let out a growl, he wanted to shock the trainer, but Entei signaled him, he didn't want them to harm humans or pokemon. Raikou remembered what Ho-oh told them and he calmed down, once they were in the house, Pikachu was running around. He wanted to play outside in the back yard. Jerry was too exhausted to do anything with his favorite pokemon as he placed Entei and Raikou down on the floor in the living room.

"Listen, you both will only be here temporarily, I won't keep you here. You both might want to be free, but right now it's too dangerous." Jerry bent down and patted Raikou on the head, then he started petting Entei, who roared at him.

" _I'm going to explode..._ " Raikou grumbled, he wanted to be free, he wanted to get to the tower, but instead they were wasting time with an unknown trainer. Entei understood how much Raikou wanted to get to the tower, to keep peace with everyone.

They had to wait a while longer until then...

* * *

In the clouds in on Mt. Faraway...

Ho-oh was looking down from the moutain, his sight was sharp, he saw that the three beasts were with trainers. It was a plan he wanted to add, he wanted them to protect two trainers and their pokemon before they started protecting more forest pokeon and other humans.

" _Once you have learned to control your powers, your real journey to the tower can begin. You can help me get those crystal silver bells back, the humans that own the tower could place them back in their rightful spot and peace will be returned..._ " Ho-oh remarked. He was spreading his wings in a tight stretch before he was peacefully asleep for the day.

* * *

Later that night...

Suicune was placed in a bed, Maria had him in her room, her mother didn't know he was there. She only knew about her own pokemon in which she trained. Suicune looked up at Maria and somehow knew she was a kind trainer like the male trainer was. Though she was very kind.

"So, I guess you like it here?" Maria looked at Suicune who only yawned and rested his head on his paws.

" _Why don't you rest, trainer... I'm not going to agree to this so easily._ " Suicune growled in his sleep, his eyes were closed. Eevee wanted to play with Suicune that night, but Maria told him that it was getting late.

" _Awww... I wanted to play with the cute baby pokemon!_ " The Eevee complained. Maria picked her pokemon up and placed him in his bed.

"Bed time." Maria whispered to her young Eevee. The Eevee let out a yawn and fell asleep finally. Maria finally had time to take a shower and get dressed for bed. Once her nightly deeds were done, she came into the room, and turned out the lights, she went into her bed and had the blankets on her, she turned off her night lamp and went to sleep.

* * *

Raikou and Entei were in the dark at Jerry's house, they were talking to each other at a voice level one, they didn't want to wake up Pikachu.

" _I think Suicune still has that rainbow feather..._ " Raikou whispered, he was angry at the situation they got into.

" _I think so too. But we don't have to worry, the trainers won't find out. We need that feather, we could have it at the tower._ " Entei purred.

" _Well, alright, I believe you. Hopefully that water head doesn't lose it..._ " Raikou hissed a bit before falling asleep, Entei only yawned and rested his head on his paws. He was soon asleep, dreaming of Ho-oh returning to them with a warm welcome.

* * *

Years later...

Entei, Raikou and Suicune were on their own again, the trainers they have protected over the years thanked them. The three beasts started roaming around and they were back together once again.

" _Man, being with a trainer is work!_ " Raikou hissed, seeing that they were young adults now, they were able to control their powers. Suicune could now make dirty rivers and dirty lakes pure again as well as being the north wind.

" _Yeah, but you get used to it._ "Suicune was keeping up with his pace. Entei was ahead of them, waiting near a moutain. There was no way around it, they would have to climb it.

" _Come on you two, no time to waste._ "Entei chuckled, the two other beasts caught up with him, they soon began making their way up the moutain, Raikou beating Entei and Suicune to the top with his lightning speed.

" _Oh god, you guys are slow..._ " Raikou teased them, he grinned.

" _We are trying!_ " Suicune let out a growl while Entei had a bit of trouble leaping, he needed to work on it. Suicune had no issue, but his speed was not a match for Raikou at all.

Once both of them reached Raikou, they looked ahead, the tower was still in sight. More pokemon below were fighting with each other. They had to stop them.

" _Well... We have more work to do..."_ Entei smiled, but he looked at a few of the humans, one of them was Professor Rein, he was caught between two Scythers. They were going to use their cut attack to kill him.

" _That guy again..."_ Raikou looked at him.

" _It's time for us to stop them, we want to keep the peace and that's what me must do._ " Suicune stated. Raikou and Entei nodded. Suicune dashed off, Entei followed him and Raikou leaped behind Entei, they came down from the mountain and landed in the area. Some more humans were sending out their pokemon to protect them from the angry wild ones.

" _I don't get why the peace is broken bewteen the humans and pokemon, but they are angry, even that Typlosion is pissed._ " Raikou looked at the one Typlosion that tried to burn a trainer, the trainer was only a young boy and his brother was proctecting him.

" _Alright, Suicune, I will need you to get on that tall rock in the middle of this meadow. The pokemon will notice you, they should stop attacking."_ Entei ordered, Suicune nodded with a low grunt and leaped away, he landed on the rock. The Scythers, Arcanines, Fearows and a few other pokemon stopped attacking the trainers and their pokemon and looked at Suicune, their anger started to slowly melt away when they realized it was him.

" _Alright guys! Let's head off! I think we pissed of this Suicune!"_ A Wigglytuff called to the pokemon. All of the wild pokemon ran back to their homes. Suicune roared and leaped off of the rock. He stood there, looking at Entei and Raikou.

Professor Rein saw them.

"It's them again, they are much bigger than the first time I saw them." He gasped as Suicune looked at him, he stood his ground, he didn't move.

" _Are you alright?_ " Suicune asked the professor. Rein walked closer to Suicune, who leaped away, he looked confused now.

"I have to follow him. I need to draw him!" Rein ran in the direction that Suicune went in. Suicune made it safely back to his friends.

" _You did well Suicune, they all listened to you._ " Entei smiled.

" _Of course, I'm the north wind._ " Suicune proudly added. Raikou hissed in annoyance.

Rein caught up with Suicune and saw that Entei and Raikou were with him.

"They are together..." Rein took out his note book and started to draw Suicune. He only had a few minutes before they would all take off, so he only had time to draw one of them. Once his drawing was completed, he closed his book and placed it back in his backpack.

He was going to make sure he collected the data for these three beasts...

* * *

 **To be continued...**

 **The next chapter might not come so soon. So if you think this story is on hiatus, it's not, if you want to check the progress on chapter 3, you can always send me a PM and I will get back to you! Nothing wrong with sending me a PM, just don't spam me. If you checked with me once this week, you can always check back next next if I give you an answer. Thank you for those that are baring with me! Again I want to thank two users for notifying me about the 11 people on here. I only knew one of them, I won't say names. But thank you guys! And thank you for reviewing this! More is to come! ^w^**


	3. Master Forces

**I know I've been gone for a bit. I have a job at a call center so it's not easy being online as often as I used to be. Thanks for baring with me on this story though, here is chapter 3!**

 **Enjoy!**

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Suicune was leading his group now, the tower wasn't in sight from below, but they knew that they would have to carry on and keep going, while making sure there was peace among humans and pokemon. Entei finally broke the silence with a low growl.

Raikou and Suicune looked back at him in alarm, then they felt like someone was watching them, they all stood their ground, waiting for something to come out from one of the bushes in the forest. Suicune braced himself while Raikou stood behind him.

" _Whatever is out here, we don't have time for it. I can sense the anger and the energy of these beings..."_ Raikou growled.

Suddenly two team rocket members came out from the bushes, they looked at the three beasts, they gave them suspicious looks and grinned at them.

"Well, well, well, this is new. I've never seen these three before, are they in the poke dex?" The team rocket girl asked, she wore a black team rocket outfit and she had blonde hair which was long enough to touch her back.

The male team rocket member took out his poke dex, he also wore a black team rocket outfit and he had aqua blue hair shaped like Trunk's hair (DBZ if your wondering...).

"No, it seems like it's says they are all un known. Their data probably isn't entered yet from those labs, but if we bring them to the boss, we could find out what they do and probably make money for our base." The male replied.

"Alright, how many master balls do we have?" The female asked, the three beasts growled at them. Before Raikou could leap at them, Entei stopped him.

" _Raikou! Stop! Peace! Remember, peace! They might seem bad, but we cannot attack them! Not without a solid reason..._ " Entei looked into Raikou's eyes. Raikou only grunted and moved back into his position.

"We only got one. So maybe if we catch one of them, we might get data for all of them. They might be the same." The male answered her question.

"Alright, Marco, are you ready to weaken two of them? We can easily catch the third one with the master ball.." The female grinned at Suicune, who scoffed at her growled, his eyes locked with hers.

" _Touch me and you'll regret it..._ " Suicune growled louder, he looked at Entei. Entei was looking at Marco with peaceful eyes. Marco didn't care, he wanted to catch him but his partner wanted Suicune.

"I'm ready for this! You will throw the master ball at one of them while I attack the blue one and the yellow one!" Marco called back.

"Alright, let's do this!" The female held out the master ball. She wanted to catch Suicune, she couldn't help it.

"Go Bayleaf!" Marco threw the quick ball as a Bayleaf came out.

"Bay!" It cried looking at the three beasts.

"Rina, catch the brown one!" Marco called to her, but it was too late, before the battle could begin, she threw the master ball at Suicune instead.

Suicune started dashing off, he tripped on a tree root below his feet, the master ball touched him. He felt the energy of the ball sucking him in.

"No! I said the brown one!" Marco called.

"Well the blue looks pretty, I couldn't help it." Rina laughed. Bayleaf sighed.

Entei and Raikou gasped as they were about to run up to Suicune and help him, but he growled at them while trying to escape the ball's pulling force.

" _NO! Both of you must run! Get away from here! I will be alright! I promise!_ " Suicune roared at them.

" _But..._ " Raikou felt tears rolling down his face. Entei backed off, beckoning Raikou to follow him.

"Stop them Bayleaf!" Marco ordered as his Bayleaf attacked Raikou, but it was injured by it's lightning attacks.

"BAAAAAY!" It cried, it was on the ground, gasping for breath.

"No!" Marco tried to run up to Entei and Raikou, but they both dashed off, never to be seen around his sight again.

"Hey, at least we got one of them." Rina held up the master ball. Suicune felt like he was in a dark place, like he died. But it felt different.

 _"My heart skipped a beat... My two friends must survive, but I will return... Some day..._ " Suicune's prayers said.

* * *

At team rocket's base...

The master ball was thrown near a cage, where Rina threw it and Suicune came out right as she locked the cage. Suicune growled at her.

"Well now, at least your not as wild. It's dangerous out there in the world." Rina reached out to pet the beast, but it backed into the corner of the cage, not wanting to be in captivity.

 _"Don't even try it... You took me away from them... You got what you wanted, you rotten trainer!_ " Suicune growled, he forgot about being peaceful, he grew darker in captivity and hoped for the best with Entei and Raikou.

"I'm not as bad as you think... We need to keep this base going, if we lose money and sales, we lose our job." Rina spoke to the Suicune but the beast could only grunt and give her a dirty look.

 _"Like your base matters. Humans and pokemon are starting to fight with each other and it's getting worse as we speak and all you can do is worry about a dumb building..._ " Suicune replied to her.

"Rina! Stop playing with Suicune and help me!" Marco called to her, he was carrying cages with more pokemon in them. Suicune saw a young Pichu with a Pikachu beside it, they were like brothers. Suicune stared at them for a long time before lying down to rest, there was nothing he could do for now.

" _If they want Entei and Raikou, they better try hard because they will never catch them..._ " Suicune looked at Rina. He started to feel like she was sort of good, but not good enough to save him from captivity.

* * *

Later...

Entei and Raikou were now walking, they were the only ones headed to the tower now.

" _What will we do? Do we just leave Suicune there with those rotten trainers!?_ " Raikou hissed, Entei stopped and sighed. He looked back at Raikou, fear was in his eyes.

" _If we go back, we might not even have a chance to save this world. Suicune told us to keep going, if he's not with us now, he'll be with his in spirit._ " Entei replied, this caused Raikou to understand why he wanted them to go without him. He saved them from the dangers of team rocket.

" _Fine, lets keep going... I want to find a cave to sleep in, my paws are tired and I'm tired from running. I'm losing energy so fast._ " Raikou grumbled between steps. Entei agreed, they needed to find a place to rest after running a long way.

Once they reached a cave, they rested together, Raikou head was on Entei back while the rest of his body rest near the ground. Entei was curled up with his head between both of his front paws. He was sleeping peacefully. From afar, Rein was drawing them, lying down next to each other.

"Now I drew them all. I must return soon, but I want to know where they are going in such a hurry... It's like they know they have some sort of a quest." Rein thought to himself.

Then he decided to see if he could touch Entei's soft fur, he wanted to know if they came from another one of his kind. He had to feel his fur to an answer, as he reached out to touch Entei, the brown beast grumbled in his sleep causing Rein to quickly rush away in fear, back into his spot in the bushes.

He didn't want to wake him up either, so he wanted to wait until he got the chance. He took out his camping supplies and made a shot fire and took out some food to eat before he rested. Following the beast was hard for him, but he wasn't going to give up. He didn't even know that Suicune was gone from their group.

* * *

At the base that night...

Suicune was sleeping, he woke up to a Pigey that was chirping, he wanted to get out of his cage and go home in the forest. Suicune woke up and yawned, he looked up at the Pigey who was making a fuss.

" _Will you please stop! I'm can't sleep with you chirping this late!_ " Suicune growled at it, the Pigey stopped chirping and looked at Suicune for a while, it finally calmed down. Suicune smiled a bit and sighed, he talked with the Pigey since he couldn't sleep.

 _"Are you in here because your new?_ " The Pigey asked him.

 _"I have no idea... But I must get out of here somehow..._ " Suicune was looking around for something that could open up his cage.

The Pigey looked around and saw a button, he didn't know what it would do. Suicune had an idea in his head.

" _Hey, do you have some bullet seed power to hit that button?_ " Suicune asked with a grinned on his face, the Pigey shook his head and pointed at Chikorita. Suicune looked at her. She was asleep.

" _Hey Chikorita! Wake up! We need your assistance over here!_ " The Pigey chirped out loud, Chikorita blinked her eyes open and yawned, he stretched and stood on her stubby feet. She looked up at her friend.

 _"What's wrong? Is someone here?_ " Chikorita looked tired as she yawned again.

 _"No! We need to hit that button on the wall that's in front of us!_ " Pigey chirped.

 _"Oh! I can use bullet seed on that button, is that what you need?_ " Chikorita started to understand his escape plan.

" _Yes ma'am!_ " Pigey replied, looking at Suicune with a wink. Suicune winked back, he watched as Chikorita used her bullet seed on the button which didn't open their cages, but they noticed water was flooding the place, the alarms went off and the members were forced to come into the base late that night so that they could get all of the pokemon out of there.

The last one that needed to be saved was Suicune, he tried to keep his head above the water, he didn't want to drown. Rina was there, he saw her, she was swimming towards his cage, she took a deep breath and dove under the water, she stuck the key in the keyhole and turned it. Suicune's cage opened as Suicune was swimming perfectly! Rina felt like she was going to drown, she was tired from swimming around te base, Suicune allowed her to ride on top of him.

 _"Hold on tight... It's not going to be easy..._ " Suicune started swimming towards the exit. Once they were outside of the base, Rina climbed off of Suicune and landed on the ground safely, she hugged Suicune and then she let go.

"You saved my life... Thank you..." Rina smiled sweetly.

Suicune looked back at her in surprise, he never had anyone do that to him before. Maybe she wasn't as bad as he thought she would be. He let out a friendly grunt, allowing her to pet him before he left.

 _"I will remember you... Release those poor pokemon and let them free. Forget about the base, it's ruined... Also, free that Chikorita and that Pigey..._ " Suicune looked at her.

"Suicune, I will free them all, I decided that he base is no longer important." Rina patted Suicune and left. The beast roared at her, she looked back at him.

" _Thank you..._ " He grunted, he turned and dashed off to find Entei and Raikou before they got into more trouble

* * *

The next morning...

Entei and Raikou were up and running, they trotted through the forest again, keeping in mind of their mission. They wanted to get all the humans and pokemon back together, without Suicune by their side, things changed, Raikou grew darker and more annoyed then normal. Entei never said anything to him. He waited for him to speak first.

" _So why are we heading to the tower again?_ " Raikou hissed.

" _I'm not sure anymore... Wait..._ " Entei realized something important.

" _Yes?_ " Raikou replied, he gave Entei a quick look for seeing a shadowed figured behind them. It's hair was waving in the wind, it was as tall as Suicune.

" _Suicune, is that you?_ " Entei squinted his eyes, seeing him. It was Suicune! He slowly walked up to them both and embraced them.

" _How in the hell did you escape?_ " Raikou wondered, he was worried.

" _I flooded their home... They had to let me go._ " Suicune replied, he still had the rainbow wing in his hair, it shined through it.

" _And I see you kept that rainbow feather. Thank god, I think it's useful._ " Entei smiled.

" _Yes, why would Ho-oh just drop it off? We would need it for luck or something..."_ Suicune chuckled, he decided that they all needed to keep on going. Rein was behind them, trying to find out where they were going.

Raikou looked back and saw Rein. He growled and turned to Suicune, who looked at the professor.

" _Him again? Is he lost or something?_ " Suicune grunted and let out a snot in annoyance. Entei looked at Suicune who only shrugged.

" _I think he's following us to the tower. He could be a big help._ " Entei walked up to the professor and bent down. He wanted to give him a ride.

"Oh? You want me to climb onto your back?" Rein proceeded to do so. Entei didn't mind having him on the team.

" _Well we better watch him..._ " Raikou said, he looked back at Rein. Rein didn't know what to think, he wanted to follow them on foot, but his plan was ruined at the moment. But he was glad to feel Entei's soft fur.

"Where are you three from? It's like I'm seeing something new." Rein asked them.

" _We don't even know..._ " Suicune sighed. It was like he woke up and saw the world, no mother or father. The same went for Entei and Raikou, no parents they were just born from out of no where.

They all walked on with nothing else to worry about...

* * *

 **To be continued...**

 **Sorry if this chapter is short, this story won't be as long either, but it is cannon for sure, so chapters 4 and 5 will be getting to point. ^w^**


	4. Revived

**Sorry for the long wait, chapter 4 is now here. I don't have much to say other than that I'm busy and I don't have as much time to write, this does not mean that I'm giving up on all my stories, it's just that the production will be much slower than normal. Thanks for understanding!**

* * *

Rein was looked to his right, he saw a couple of Butterfree on the way to the tower. They were pretty upset as they were going after someone. This caused Entei to rush and break into a run, Rein who was hanging onto him loosely, held on to him tightly now.

Suicune was the first one to reach the edge of the tower as he noticed it, he looked up as he realized that it was so many stories high. He grunted and looked back, he waited for Raikou and Entei to show up.

" _Hurry up you two, we might not be able to stop these other pokemon unless we go inside this tower..._ " Suicune grunted at them, Raikou and Entei were finally close enough that they both allowed Rein to walk around freely.

"So what do you three have to do with this tower?" Rein turned and looked at Entei. The large pokemon shook his head, he didn't know the answer but he did know that something was wrong with the tower and the pokemon were going inside of it to attack someone.

" _We need to hurry and save the one that these crazy pokemon are after!_ " Raikou roared as he dashed off, leaving Rein behind, but he soon followed them inside, a young boy was int he tower. He was holding onto four silver bells.

A Mankey was coming up from behind him along with a few Butterfree and some angry Eevees.

"Leave me alone, please!" The young boy cried, he dropped some poke balls as a few of his own pokemon came out and protected him.

"Meowth?" The young boy looked up at his shiny Meowth. It mewled in anger and threw coins at all of the pokemon that were trying to attack him. His other pokemon, Jolteon came out and used it's thunder shock to paralyze the Butterfree, but they were using stun spore against the small party.

Finally, Raikou leaped in and protected the young boy, he stood his ground and allowed the pokemon to strike at him while Suicune roared, causing them all to go after him. Entei leaped on an angry Scyther that was about to cut the shiny Meowth in half.

The Meowth covered it's eyes in fear, seeing that it's attacks didn't work for too long. Raikou shocked the Evees as they took off in fear. Umbreon was ready to attack as it came near the thunder beast. Raikou roared at it as it was forced down the stairs of the tower. So many people from the outside came to the tower that morning for a tour, but so many angry pokemon were escaping the tower to attack them instead.

"Why are they all attacking you?" Rein was able to reach the young boy.

"They were after the silver bells, I dropped them all by mistake and I was trying to put them back up, but the hooks are too high on every corner." The young boy slowly got to his feet, he called his pokemon back into their poke balls.

"Who was after the silver bells, young one?" Rein asked. He began to hold the boy against him tightly.

"Team rocket! They were after the silver bells and then I had my small team take care of them! That's when all of these pokemon started to get angry!" The young boy cried.

"It looks like we will have to stop this! But first, let's get you out of here!" Rein took his sketch book and grabbed the young boy's arm and lead him down the stairs where a growlithe growled at them.

"Oh no!" The young boy cried in fear, he hugged Rein tightly. Rein took out his timer ball while the young boy's pokemon came to their aid and got ready to pounce on the pokemon blocking their path.

"Go Rhydon!" Rein shouted. The Rhydon came out of the timer ball and roared before it was given orders.

"Roar!" It roared, looking down at the growlithe who was about to attack it, but the Rhydon slapped it so hard it flew out of the tower and on the ground, defeated.

"Whoa! You didn't have to tell it anything." The boy looked surprised as he returned his pokemon back into the poke balls. Rein thanked his Rhydon and got on it's back.

"You too, come on." Rein helped the boy up as the Rhydon dashed through the bottom floor of the tower and smashed into a lot of angry pokemon. Seal was knocked over as it slammed into a slowpoke and it fell over. The more they fought, the worse things got.

* * *

Mean while...

Entei and Raikou were up against an angry persian that didn't want to give in. It used hyper beam on Entei. Raikou looked at Entei in shock, it made him upset to see that another pokemon attacked his friend.

Raikou roared and attacked the persian, biting into it's neck and throwing it out of the tower window. It fell and banged it's head against the ground, it was defeated as it growled and ran away in anger.

Without the special bird pokemon in sight, all they could do was fight. Suicune was fighting against a dewgong, he used his ice beam to freeze it, but it dodged all of his attacks swiftly and pounded him to the floor. Suicune felt like blood was running down his leg from the bite he received from dewgong's ice fang attack.

" _Damn... If I keep on fighting like this, I'm not going to save that kid, or this tower._ " Suicune thought as he kicked the dewgong in the belly, scratching it with his back paws as it wailed in pain and ran away.

* * *

Near the entrance...

Team rocket made their way to the tower, they had a pack of matches and some fire wood. They even had a charizard with them as well as a dragonite to add more spice to the battle between the pokemon and the people.

"Well, it looks like we got here in time." One of the members grinned.

"The tower is going down! If those pokemon won't stop, we will stop it and we will get those beasts!" A female member laughed.

Rein was writing in his book about how the beasts were saving the tower, they were meant to protect it and the four silver bells. He watched the young boy and his mother, they were scared for the beasts that were there. When Rein turned to his left, he saw team rocket, they were carrying supplies that included some matches, fire wood and two pokemon that could do damage and cause a fire. Rein dropped his book quickly and ran over to team rocket.

"NO! What are you all doing!? You all can't blow up the tower and burn it!" Rein shouted at them.

"If you are willing to get burned, I suppose you back off!" A male member grinned at him and carelessly told his charizard to use flamethrower at the tower as the rest of the members lit up their matches and placed fire on the fire wood and they threw the burning wood at the tower. The small flames started to grow around the sides of the tower. As everyone gasped, they backed away a few feet to avoid getting burned, before the flames got to the front, Rein jumped back into the tower. He was going to try and save the beasts as they finished off the last pokemon which was a kadabra, it teleported out of the tower as Rein went up the stairs and saw the three beasts looking at the flames in fear.

"Follow me!" Rein called as a support beam came down and was about to fall on him, Suicune pushed him out of the way as quickly leaped back as the beam fell and hit the wooden floor hard.

Entei looked at Suicune who was about to leap over the support beam first to get Rein to safety but more wood blocked their path as Entei roared at Rein.

" _Go! Get out of here! We will find a way out!_ " Entei roared to Rein. Rein felt tears escaping his eyes, he wanted to them get out as his Rhydon came back for him and made him leave the tower, it gave him a ride as they made it out. From the outside, the tower was burning with flames. Suicune looked at Entei with a concerned look on his face, Raikou did the same. Entei closed his eyes as Suicune and Raikou huddled up against him. They could not breathe in the fire for too long. By the time the tower was ready to collapse, Entei and his two friends felt the tower's roof coming down. Lots of wood fell to the floor as Suicune saw Entei and Raikou one last time before his vision blacked out quickly. Raikou and Entei suffered the same fate.

The tower finally collapsed to the ground as Rein saw this, he shouted.

"Nooooooo!" This can't be happening!" Rein picked up his things and ran to were the beasts were, under all of the wood and ash. Everyone kept their distance, they looked sad as many others started crying.

From under the wood, Suicune had wood in his right eye, it went through his skull. Raikou had a huge piece of wood lodged through his heart and out of his back while Entei suffered more damage, there wood that went through his sides, back, chest and through both eyes. Rein was able to uncover Suicune as he gasped.

"This can't be happening..." Rein covered his mouth.

"Are they alright?" A lady asked.

"I'm afraid not..." Rein walked over to all of the people. He was sad, he wanted to prevent this from happening as team rocket was laughing.

"You think you could have saved them? It was either we catch them or we kill them!" A team rocket member laughed.

"No... No! You all are complete murderers! You got them killed! They were trying to save the tower! And you did this because you wanted to the four silver bells!" Rein growled at them.

"Yes, that what we all came here for. When we took those beasts we wanted the silver bells and they were going to guide us to them, but since we could not have them, we burned the tower." The female team rocket member laughed. Their team left and went back to their base.

"You all will pay for this!" Rein growled.

The young boy still had the four silver bells with him. He walked over to Rein.

"I still got the silver bells. It was either they burn the tower or I give them what they want. I wanted peace so giving them the bells was a hard decision, sir." The boy sniffled.

"I understand. At least those beasts protected us. They did what they were supposed to do. I believe they were also trying to get people and pokemon together. But right now, it's not like that. It was never like that to begin with when team rocket started to step in.

"What's going to happen?" The boy asked, he we concerned about Entei, Raikou and Suicune.

Before Rein could answer that, a huge beam of light from the sky centered around the broken down tower. Rein opened his eyes.

"It's him! It's really him!" Rein cried.

"What do you mean? You know that bird?" The boy was now confused.

Everyone gasped, the bird seemed to look like a god. Like a legend.

"It's Ho-Oh. Legends say that it comes when a rainbow feather is near. But why is it here without a rainbow feather?" Rein wondered then it dawned on him that one of the beasts may have been carrying one. He looked back at the wood pile saw a piece of rainbow colors sticking out of it. Then he looked above and saw Ho-Oh flying over the burnt down tower. It closed it's eyes and did something magical. Dust was coming down. All of the people begin to wonder what was happening. As the light faded, Ho-Oh let out a squawk and flew away, until he was gone from their sight. Everyone looked back down at the pile of ash and wood as the wood shifted a little. A gray paw came out along with a blue and yellow paw. Then the wood fully shifted as the three beasts looked normal. They jumped out of the ashes and the wood.

"No, it can't be! They were..." Rein looked at them in surprise.

"Dead? I thought so too..." The boy stopped crying as he smiled at all three of the beasts.

Entei, Raikou and Suicune let out a roar to the people as they saw that all of the pokemon that were angry came back feeling happy and sorry for what they caused. The silver bells were together and the pokemon agreed to be friendly.

"They did it..." Rein smiled as waved to them. Entei, Raikou and Suicune looked to the right ad saw Rein waving at them. They gave him a smile but then turned back to the rest of of the townsfolk and roared again. After that, they all went their separate ways, protecting pokemon of their own type as well as protecting all of the people.

When Rein got home that day, he heard the news on the tower. The tower was going to be built back up again and the silver bells were going to be on the third floor of the tower instead of the second floor. Rein felt relieved to hear about the tower being built up again. He finally knew that all three of the beasts had a connection to the tower and that Ho-Oh saved them from death.

"Until we meet again..." Rein closed his sketch book. He was planning on meeting the professor about his findings the next day since today was tiring for him.

* * *

 **The End.**

 **Well I wanted to end it here because I said that I would be getting to the point. There might be another story that connects with this one, but who knows, I'm not good at writing pokemon stories as I need to work on it a bit more. Also for the next few stories after I get the one about the Raikou out of way, I will be doing the normal pokemon with the legendaries in it but the legendaries will not be the main characters, instead more of side characters and rare appearances. Thanks to those that read this!**


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